genomic islands

[mmmm]

hi all- is there a softwrae that is used to determine (genomic islands) within the draft assembled bacterial genomes?- thanks all

[maubp]

There are lots of approaches, often based on comparison to several close relatives to find novel genes not in the relatives. If these form clusters they are candidates for horizontally acquired islands - although if in a lone contig you might also suspect contamination.

[mmmm]

thanks- what is the fastest approach to determine unique genes (specially genomic islands) within the assembled draft genomes

[mmmm]

what is the software can tell about genomic islands (no. size, etc) in relation to the reference bacterial genome please?

[DrX]

You'll just need to pick out differences manually. Use a visual genome aligner like Mauve to compare your genome against a reference. You can even get as simple as a straight up dotplot. Large genetic insertions should be blindingly obvious.

[yzzhang]

Here is a review listing the methods to detect genomic islands http://www.nature.com/nrmicro/journa...micro2350.html